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Author SHA1 Message Date
Ricardo Wurmus
15f98b0d23
gnu: Add r-erma. 
* gnu/packages/bioinformatics.scm (r-erma): New variable.
 2017-11-07 23:32:43 +01:00
Ricardo Wurmus
421c68e3f7
gnu: Add r-homo-sapiens. 
* gnu/packages/bioinformatics.scm (r-homo-sapiens): New variable.
 2017-11-07 23:32:43 +01:00
Ricardo Wurmus
b52a866d14
gnu: Add r-org-hs-eg-db. 
* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): New variable.
 2017-11-07 23:32:43 +01:00
Ricardo Wurmus
dd5fc8b78e
gnu: Add r-snpstats. 
* gnu/packages/bioinformatics.scm (r-snpstats): New variable.
 2017-11-07 23:32:43 +01:00
Ricardo Wurmus
e2b927993e
gnu: Add r-gqtlbase. 
* gnu/packages/bioinformatics.scm (r-gqtlbase): New variable.
 2017-11-07 23:32:43 +01:00
Ricardo Wurmus
96a392a0b2
gnu: Add r-gprofiler. 
* gnu/packages/bioinformatics.scm (r-gprofiler): New variable.
 2017-11-07 23:32:42 +01:00
Ricardo Wurmus
60faf94597
gnu: Add r-ggbio. 
* gnu/packages/bioinformatics.scm (r-ggbio): New variable.
 2017-11-07 23:32:42 +01:00
Ricardo Wurmus
7af1f40373
gnu: Add r-biovizbase. 
* gnu/packages/bioinformatics.scm (r-biovizbase): New variable.
 2017-11-07 23:32:42 +01:00
Ricardo Wurmus
2f6f61fd8e
gnu: Add r-organismdbi. 
* gnu/packages/bioinformatics.scm (r-organismdbi): New variable.
 2017-11-07 23:32:42 +01:00
Ricardo Wurmus
aa30ab5aee
gnu: Add r-ensembldb. 
* gnu/packages/bioinformatics.scm (r-ensembldb): New variable.
 2017-11-07 23:32:42 +01:00
Ricardo Wurmus
763e98103a
gnu: Add r-annotationfilter. 
* gnu/packages/bioinformatics.scm (r-annotationfilter): New variable.
 2017-11-07 23:32:42 +01:00
Ricardo Wurmus
04e2a2e969
gnu: Add r-dirichletmultinomial. 
* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): New variable.
 2017-11-07 23:32:41 +01:00
Ricardo Wurmus
3af149f524
gnu: Add r-complexheatmap. 
* gnu/packages/bioinformatics.scm (r-complexheatmap): New variable.
 2017-11-07 23:32:41 +01:00
Ricardo Wurmus
902fb15d92
gnu: Add r-genomicfiles. 
* gnu/packages/bioinformatics.scm (r-genomicfiles): New variable.
 2017-11-07 23:32:41 +01:00
Marius Bakke
cd215877a0
gnu: bdftopcf: Update to 1.1. 
* gnu/packages/xorg.scm (bdftopcf): Update to 1.1.
[native-inputs]: Change from LIBXFONT to LIBXFONT2.
 2017-11-07 23:29:23 +01:00
Marius Bakke
d469bc09bd
gnu: feh: Update to 2.22.2. 
* gnu/packages/image-viewers.scm (feh): Update to 2.22.2.
 2017-11-07 22:16:27 +01:00
Jan Nieuwenhuizen
625492ee1a
gnu: gcc-4.7: Resurrect building with gcc-5.4.0. 
* gnu/packages/patches/gcc-4-compile-with-gcc-5.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/gcc.scm (gcc-4.7): Use it.
 2017-11-07 22:03:51 +01:00
Rutger Helling
a67f094671
gnu: Add websockify. 
* gnu/packages/web.scm (websockify): New variable.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2017-11-07 21:56:42 +01:00
Gábor Boskovits
75d342ffa9
gnu: Add python-networkx2. 
* gnu/packages/python.scm (python-networkx2, python2-networkx2): New variables.
* gnu/local.mk (dist_patch_DATA): Register 'python-networkx2-reproducible-build.patch'.
* gnu/packages/patches/python-networkx2-reproducible-build.patch: New file.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2017-11-07 21:17:20 +01:00
Gábor Boskovits
2b295f5a2f
gnu: Add python-pydot. 
* gnu/packages/graphviz.scm (python-pydot, python2-pydot): New variables.

Modified-by: Marius Bakke <mbakke@fastmail.com>
 2017-11-07 21:03:15 +01:00
Marius Bakke
38ad27da80
gnu: mercurial: Update to 4.4.1. 
* gnu/packages/version-control.scm (mercurial): Update to 4.4.1.
 2017-11-07 20:23:29 +01:00
Marius Bakke
4a30c1c0e2
gnu: vim: Update to 8.0.1274 [fixes CVE-2017-1000382]. 
* gnu/packages/vim.scm (vim): Update to 8.0.1274.
 2017-11-07 20:21:46 +01:00
Marius Bakke
31a963fe80
gnu: notmuch: Update to 0.25.2. 
* gnu/packages/mail.scm (notmuch): Update to 0.25.2.
 2017-11-07 20:01:03 +01:00
Efraim Flashner
9129804230
gnu: psm: Only use as an input on supported-systems. 
Syntax help supplied by bavier@member.fsf.org

* gnu/packages/linux.scm (libfabric)[inputs]: Only use psm as an input
on systems where psm is supported.
* gnu/packages/mpi.scm (openmpi)[inputs]: Same.
 2017-11-07 20:41:08 +02:00
Efraim Flashner
b516b78002
gnu: psm: Limit supported systems. 
* gnu/packages/linux.scm (psm)[supported-systems]: New field, limit to
i686-linux and x86_64-linux.
 2017-11-07 20:41:05 +02:00
Efraim Flashner
174807b9a4
gnu: gnupg: Update to 2.2.2. 
* gnu/packages/gnupg.scm (gnupg): Update to 2.2.2.
 2017-11-07 19:34:29 +02:00
Efraim Flashner
2f17187ff3
gnu: mediainfo: Change order of custom phases. 
* gnu/packages/video.scm (mediainfo)[arguments]: Change to the build
directory before executing the autogen script.
 2017-11-07 19:34:25 +02:00
Mathieu Othacehe
6541673354
gnu: linux: Fix kconfig selection. 
* gnu/packages/linux.scm (make-linux-libre): When cross-compiling,
  "kconfig" field is in native-inputs variable. So config is always #f
  when cross-compiling linux.
 2017-11-07 18:16:02 +01:00
Dave Love
f4433d09a1
gnu: openmpi: Add dependency on PSM. 
* gnu/packages/mpi.scm (openmpi)[inputs]: Add PSM.
 2017-11-07 18:09:13 +01:00
Dave Love
7bc05ef0ac
gnu: libfabric: Add dependency on PSM. 
* gnu/packages/linux.scm (libfabric)[inputs]: Add PSM.
 2017-11-07 18:09:13 +01:00
Dave Love
fd23d259cd
gnu: Add PSM. 
* gnu/packages/linux.scm (psm): New variable.
* gnu/packages/patches/psm-arch.patch,
gnu/packages/patches/psm-ldflags.patch,
gnu/packages/patches/psm-repro.patch: New files.
* gnu/local.mk (dist_patch_DATA): Add them.
 2017-11-07 18:09:13 +01:00
Gábor Boskovits
63b7fbe1bb
gnu: diffoscope: Update to 88. 
* gnu/packages/package-management.scm (diffoscope): Update to 88.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-11-07 18:09:13 +01:00
ng0
db0164b21f
gnu: awesome: Update to 4.2. 
* gnu/packages/wm.scm (awesome): Update to 4.2.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-11-07 18:09:13 +01:00
Timothy Sample
3eda8dd614
services: gdm: Add environment variables. 
While not an optimal solution (see comment), this makes GDM functional.

* gnu/services/xorg.scm (gdm-shepherd-service): Set PATH and XDG_DATA_DIRS
environment variables.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-11-07 18:09:13 +01:00
Timothy Sample
51bc8357e8
gnu: gdm: Add configure flags for better defaults. 
* gnu/packages/gnome.scm (gdm)[arguments]<#:configure-flags>: Add
--with-initial-vt=7 and --enable-gdm-xsession.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-11-07 18:09:13 +01:00
Timothy Sample
950d8e5d8c
gnu: gdm: Fix config file path. 
* gnu/packages/gnome.scm (gdm)[arguments]<#:phases>: Fix the
'pre-configure phase so that GDM finds its config file.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-11-07 18:09:13 +01:00
Oleg Pykhalov
ad54924285
gnu: expect: Change home-page to http://expect.sourceforge.net/. 
* gnu/packages/tcl.scm (expect): Change home-page to
  http://expect.sourceforge.net/.
 2017-11-07 18:50:46 +03:00
Ricardo Wurmus
e160aa1f81
gnu: Add r-gage. 
* gnu/packages/bioinformatics.scm (r-gage): New variable.
 2017-11-07 12:39:51 +01:00
Ricardo Wurmus
3121814ef1
gnu: Add r-keggrest. 
* gnu/packages/bioinformatics.scm (r-keggrest): New variable.
 2017-11-07 12:39:51 +01:00
Ricardo Wurmus
a9540107c6
gnu: antlr3-3.3: Prettify build phases. 
* gnu/packages/java.scm (antlr3-3.3)[arguments]: Prettify build phases
"bin-install" and "generate-grammar".
 2017-11-07 12:39:50 +01:00
Ricardo Wurmus
9ecc4c69eb
gnu: r-servr: Update to 0.8. 
* gnu/packages/web.scm (r-servr): Update to 0.8.
 2017-11-07 08:15:45 +01:00
Ricardo Wurmus
60ec9da3aa
gnu: r-tidyselect: Update to 0.2.3. 
* gnu/packages/statistics.scm (r-tidyselect): Update to 0.2.3.
 2017-11-07 08:15:44 +01:00
Ricardo Wurmus
baa00ee90d
gnu: r-msnbase: Update to 2.4.0. 
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.4.0.
[propagated-inputs]: Add r-lattice; remove r-reshape2.
 2017-11-07 08:15:44 +01:00
Ricardo Wurmus
39d9098def
gnu: r-mutationalpatterns: Update to 1.4.0. 
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.4.0.
[propagated-inputs]: Add r-cowplot, r-ggdendro, and r-s4vectors.
 2017-11-07 08:15:44 +01:00
Ricardo Wurmus
14b3c71911
gnu: r-annotationhub: Update to 2.10.0. 
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.10.0.
[propagated-inputs]: Add r-curl.
 2017-11-07 08:15:44 +01:00
Ricardo Wurmus
15ca195979
gnu: r-mzr: Remove bundled copy of boost. 
* gnu/packages/bioinformatics.scm (r-mzr)[source]: Remove boost source.
[arguments]: Add build phase "use-system-boost" to link with our boost
package and avoid building the bundled sources.
 2017-11-07 08:15:44 +01:00
Ricardo Wurmus
34b9675449
gnu: r-mzr: Update to 2.12.0. 
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.12.0.
 2017-11-07 08:15:43 +01:00
Ricardo Wurmus
b500dbcdef
gnu: r-mzid: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-mzid): Update to 1.16.0.
 2017-11-07 08:15:43 +01:00
Ricardo Wurmus
eeaa6967f9
gnu: r-chipseq: Update to 1.28.0. 
* gnu/packages/bioinformatics.scm (r-chipseq): Update to 1.28.0.
[propagated-inputs]: Add r-lattice.
 2017-11-07 08:15:43 +01:00
Ricardo Wurmus
158b6743dc
gnu: r-genomicfeatures: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.30.0.
[propagated-inputs]: Add r-rmysql.
 2017-11-07 08:15:43 +01:00
Ricardo Wurmus
74248d22a0
gnu: Add r-rmysql. 
* gnu/packages/databases.scm (r-rmysql): New variable.
 2017-11-07 08:15:43 +01:00
Ricardo Wurmus
4dd469ef6d
gnu: r-rtracklayer: Update to 1.38.0. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.38.0.
[arguments]: Adjust patch to use system zlib.
 2017-11-07 08:15:42 +01:00
Ricardo Wurmus
a044c7f4c4
gnu: r-biocparallel: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.12.0.
[propagated-inputs]: Add r-bh.
 2017-11-07 08:15:42 +01:00
Ricardo Wurmus
42e11d3301
gnu: r-biomart: Update to 2.34.0. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.34.0.
[propagated-inputs]: Add r-progress and r-stringr.
 2017-11-07 08:15:42 +01:00
Ricardo Wurmus
010ab2ffd2
gnu: r-edger: Update to 3.20.1. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.20.1.
[propagated-inputs]: Add r-rcpp.
 2017-11-07 08:15:42 +01:00
Ricardo Wurmus
eb3f5cc76a
gnu: r-gostats: Update to 2.44.0. 
* gnu/packages/bioinformatics.scm (r-gostats): Update to 2.44.0.
[propagated-inputs]: Add r-rgraphviz.
 2017-11-07 08:15:41 +01:00
Ricardo Wurmus
2404cc4283
gnu: r-category: Update to 2.44.0. 
* gnu/packages/bioinformatics.scm (r-category): Update to 2.44.0.
[propagated-inputs]: Remove r-rsqlite; add r-dbi.
 2017-11-07 08:15:41 +01:00
Ricardo Wurmus
65a8cd6676
gnu: r-lubridate: Update to 1.7.1. 
* gnu/packages/statistics.scm (r-lubridate): Update to 1.7.1.
[propagated-inputs]: Add r-rcpp.
 2017-11-07 08:15:41 +01:00
Ricardo Wurmus
689edf1153
gnu: r-preprocesscore: Update to 1.40.0. 
* gnu/packages/statistics.scm (r-preprocesscore): Update to 1.40.0.
 2017-11-07 08:15:41 +01:00
Ricardo Wurmus
e7f680f071
gnu: r-r-utils: Update to 2.6.0. 
* gnu/packages/statistics.scm (r-r-utils): Update to 2.6.0.
 2017-11-07 08:15:41 +01:00
Ricardo Wurmus
ecfe98a17a
gnu: r-openssl: Update to 0.9.8. 
* gnu/packages/statistics.scm (r-openssl): Update to 0.9.8.
 2017-11-07 08:15:40 +01:00
Ricardo Wurmus
aced057fbc
gnu: r-rlang: Update to 0.1.4. 
* gnu/packages/statistics.scm (r-rlang): Update to 0.1.4.
 2017-11-07 08:15:40 +01:00
Ricardo Wurmus
1be0f53664
gnu: r-vsn: Update to 3.46.0. 
* gnu/packages/bioinformatics.scm (r-vsn): Update to 3.46.0.
[propagated-inputs]: Remove r-hexbin.
 2017-11-07 08:15:40 +01:00
Ricardo Wurmus
007424b5a5
gnu: r-motifrg: Rename input label. 
* gnu/packages/bioinformatics.scm (r-motifrg)[propagated-inputs]:
Rename label of r-bsgenome-hsapiens-ucsc-hg19.
 2017-11-07 08:15:40 +01:00
Ricardo Wurmus
ce59d62519
gnu: r-motifrg: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.22.0.
 2017-11-07 08:15:40 +01:00
Ricardo Wurmus
98791c25c8
gnu: r-qvalue: Update to 2.10.0. 
* gnu/packages/bioinformatics.scm (r-qvalue): Update to 2.10.0.
 2017-11-07 08:15:39 +01:00
Ricardo Wurmus
87fa5aface
gnu: r-fastseq: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-fastseq): Update to 1.24.0.
 2017-11-07 08:15:39 +01:00
Ricardo Wurmus
1567c8d91b
gnu: r-interactivedisplaybase: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Update to
1.16.0.
 2017-11-07 08:15:39 +01:00
Ricardo Wurmus
0096127974
gnu: r-edaseq: Update to 2.12.0. 
* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.12.0.
 2017-11-07 08:15:39 +01:00
Ricardo Wurmus
22752bef3b
gnu: r-msnid: Update to 1.11.0. 
* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.11.0.
 2017-11-07 08:15:38 +01:00
Ricardo Wurmus
8140f680ad
gnu: r-deseq: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-deseq): Update to 1.30.0.
 2017-11-07 08:15:38 +01:00
Ricardo Wurmus
531e80903f
gnu: r-aroma-light: Update to 3.8.0. 
* gnu/packages/bioinformatics.scm (r-aroma-light): Update to 3.8.0.
 2017-11-07 08:15:38 +01:00
Ricardo Wurmus
a998c9a464
gnu: r-pcamethods: Update to 1.70.0. 
* gnu/packages/bioinformatics.scm (r-pcamethods): Update to 1.70.0.
 2017-11-07 08:15:38 +01:00
Ricardo Wurmus
8a8138d248
gnu: r-affyio: Update to 1.48.0. 
* gnu/packages/bioinformatics.scm (r-affyio): Update to 1.48.0.
 2017-11-07 08:15:38 +01:00
Ricardo Wurmus
dad5f83817
gnu: r-affy: Update to 1.56.0. 
* gnu/packages/bioinformatics.scm (r-affy): Update to 1.56.0.
 2017-11-07 08:15:37 +01:00
Ricardo Wurmus
9a665dfb6f
gnu: r-protgenerics: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-protgenerics): Update to 1.10.0.
 2017-11-07 08:15:37 +01:00
Ricardo Wurmus
617700895b
gnu: r-seqlogo: Update to 1.44.0. 
* gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.44.0.
 2017-11-07 08:15:37 +01:00
Ricardo Wurmus
e127c918f8
gnu: r-genomation: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.10.0.
[propagated-inputs]: Remove r-rhtslib.
[inputs]: Remove zlib.
 2017-11-07 08:15:37 +01:00
Ricardo Wurmus
e6ce4bf00d
gnu: r-impute: Update to 1.52.0. 
* gnu/packages/bioinformatics.scm (r-impute): Update to 1.52.0.
 2017-11-07 08:15:37 +01:00
Ricardo Wurmus
0f948b116b
gnu: r-seqpattern: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.10.0.
 2017-11-07 08:15:36 +01:00
Ricardo Wurmus
e67850b40d
gnu: r-bsgenome: Update to 1.46.0. 
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.46.0.
 2017-11-07 08:15:36 +01:00
Ricardo Wurmus
d13a3fea7e
gnu: r-topgo: Update to 2.30.0. 
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.30.0.
 2017-11-07 08:15:36 +01:00
Ricardo Wurmus
aeb73879f6
gnu: r-graph: Update to 1.56.0. 
* gnu/packages/bioinformatics.scm (r-graph): Update to 1.56.0.
 2017-11-07 08:15:36 +01:00
Ricardo Wurmus
96fb465174
gnu: r-genomicalignments: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.14.0.
 2017-11-07 08:15:35 +01:00
Ricardo Wurmus
6fcbed7329
gnu: r-summarizedexperiment: Update to 1.8.0. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.8.0.
 2017-11-07 08:15:35 +01:00
Ricardo Wurmus
cb0a9a7493
gnu: r-delayedarray: Update to 0.4.1. 
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.4.1.
 2017-11-07 08:15:35 +01:00
Ricardo Wurmus
f8068419a6
gnu: r-rsamtools: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.30.0.
 2017-11-07 08:15:35 +01:00
Ricardo Wurmus
b719435ebb
gnu: r-biostrings: Update to 2.46.0. 
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.46.0.
 2017-11-07 08:15:35 +01:00
Ricardo Wurmus
0f8d98f294
gnu: r-annotationdbi: Update to 1.40.0. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.40.0.
 2017-11-07 08:15:34 +01:00
Ricardo Wurmus
ca52123611
gnu: r-biobase: Update to 2.38.0. 
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.38.0.
 2017-11-07 08:15:34 +01:00
Ricardo Wurmus
aa5c1f61f1
gnu: r-genomicranges: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.30.0.
 2017-11-07 08:15:34 +01:00
Ricardo Wurmus
2b6ae8bfd5
gnu: r-xvector: Update to 0.18.0. 
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.18.0.
 2017-11-07 08:15:34 +01:00
Ricardo Wurmus
f642c0e4c7
gnu: r-limma: Update to 3.34.0. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.34.0.
 2017-11-07 08:15:33 +01:00
Ricardo Wurmus
7f1bac3528
gnu: r-variantannotation: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.24.0.
 2017-11-07 08:15:33 +01:00
Ricardo Wurmus
8aab0235e0
gnu: r-genomeinfodb: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.14.0.
 2017-11-07 08:15:33 +01:00
Ricardo Wurmus
9e482c2069
gnu: r-iranges: Update to 2.12.0. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.12.0.
 2017-11-07 08:15:33 +01:00
Ricardo Wurmus
41f0f94976
gnu: r-s4vectors: Update to 0.16.0. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.16.0.
 2017-11-07 08:15:33 +01:00
Ricardo Wurmus
2167eafc1d
gnu: r-biocstyle: Update to 2.6.0. 
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.6.0.
 2017-11-07 08:15:32 +01:00
Ricardo Wurmus
3241461670
gnu: r-biocinstaller: Update to 1.28.0. 
* gnu/packages/bioinformatics.scm (r-biocinstaller): Update to 1.28.0.
 2017-11-07 08:15:32 +01:00
Ricardo Wurmus
d61fc4e104
gnu: r-biocgenerics: Update to 0.24.0. 
* gnu/packages/bioinformatics.scm (r-biocgenerics): Update to 0.24.0.
 2017-11-07 08:15:32 +01:00
Ricardo Wurmus
704fe4d115
gnu: r-grohmm: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.12.0.
 2017-11-07 08:15:32 +01:00
Ricardo Wurmus
843826e262
gnu: r-shortread: Update to 1.36.0. 
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.36.0.
 2017-11-07 08:15:31 +01:00
Ricardo Wurmus
b53755258a
gnu: r-systempiper: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.12.0.
 2017-11-07 08:15:31 +01:00
Ricardo Wurmus
9f52e53d5d
gnu: r-gseabase: Update to 1.40.0. 
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.40.0.
 2017-11-07 08:15:31 +01:00
Ricardo Wurmus
fad7c0c7bd
gnu: r-sva: Update to 3.26.0. 
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.26.0.
 2017-11-07 08:15:31 +01:00
Ricardo Wurmus
91e1867972
gnu: r-methylkit: Update to 1.4.0. 
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.4.0.
 2017-11-07 08:15:31 +01:00
Ricardo Wurmus
c126ba69db
gnu: r-copywriter: Update to 2.10.0. 
* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.10.0.
 2017-11-07 08:15:30 +01:00
Ricardo Wurmus
598dacf657
gnu: r-annotationfilter: Update to 1.2.0. 
* gnu/packages/bioinformatics.scm (r-annotationfilter): Update to 1.2.0.
 2017-11-07 08:15:30 +01:00
Ricardo Wurmus
e6b332d43b
gnu: r-rhdf5: Update to 2.22.0. 
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.22.0.
 2017-11-07 08:15:30 +01:00
Ricardo Wurmus
19e8929cbd
gnu: r-tximport: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.6.0.
 2017-11-07 08:15:30 +01:00
Ricardo Wurmus
da153b7f94
gnu: r-bamsignals: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.10.0.
 2017-11-07 08:15:30 +01:00
Ricardo Wurmus
5c18470008
gnu: r-zlibbioc: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.24.0.
 2017-11-07 08:15:29 +01:00
Ricardo Wurmus
1d0263b44e
gnu: r-rhtslib: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.10.0.
 2017-11-07 08:15:29 +01:00
Ricardo Wurmus
c25154e5cb
gnu: r-rbgl: Update to 1.54.0. 
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.54.0.
 2017-11-07 08:15:29 +01:00
Ricardo Wurmus
727706ad38
gnu: r-annotationforge: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.20.0.
 2017-11-07 08:15:29 +01:00
Ricardo Wurmus
3fd010ff30
gnu: r-dexseq: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.24.0.
 2017-11-07 08:15:28 +01:00
Ricardo Wurmus
0166dc07ef
gnu: r-deseq2: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.18.0.
 2017-11-07 08:15:28 +01:00
Ricardo Wurmus
554fac74aa
gnu: r-genefilter: Update to 1.60.0. 
* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.60.0.
 2017-11-07 08:15:28 +01:00
Ricardo Wurmus
cb4d3ff2c4
gnu: r-geneplotter: Update to 1.56.0. 
* gnu/packages/bioinformatics.scm (r-geneplotter): Update to 1.56.0.
 2017-11-07 08:15:28 +01:00
Ricardo Wurmus
2d4e887dc0
gnu: r-annotate: Update to 1.56.0. 
* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.56.0.
 2017-11-07 08:15:28 +01:00
Ricardo Wurmus
94fd86e5e1
gnu: r-dnacopy: Update to 1.52.0. 
* gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.52.0.
 2017-11-07 08:15:27 +01:00
Ricardo Wurmus
c7782c3f1f
gnu: r-biocviews: Update to 1.46.0. 
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.46.0.
[propagated-inputs]: Remove r-knitr.
 2017-11-07 08:15:27 +01:00
Ricardo Wurmus
7373b4167a
gnu: r-bioccheck: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.14.0.
[native-inputs]: Remove which.
[propagated-inputs]: Add r-stringdist.
 2017-11-07 08:15:27 +01:00
Ricardo Wurmus
a40a04fdbb
gnu: Add r-stringdist. 
* gnu/packages/cran.scm (r-stringdist): New variable.
 2017-11-07 08:15:27 +01:00
Ricardo Wurmus
8ca2b2b06e
gnu: r-rgraphviz: Update to 2.22.0. 
* gnu/packages/graph.scm (r-rgraphviz): Update to 2.22.0.
 2017-11-07 08:15:27 +01:00
Ludovic Courtès
a0e4b41b40
gnu: guile-git: Update snapshot. 
* gnu/packages/guile.scm (guile-git): Update to commit 951a32c.
 2017-11-07 00:12:11 +01:00
Brendan Tildesley
fedde43b6d
gnu: moka-icon-theme: Fix license. 
* gnu/packages/gnome.scm (moka-icon-theme): Add cc-by-sa4.0 to license field.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-11-07 00:12:11 +01:00
Brendan Tildesley
550281fb5f
gnu: moka-icon-theme: Add faba-icon-theme as propagated input. 
* gnu/packages/gnome.scm (moka-icon-theme)[propagated-inputs]: New field.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-11-07 00:12:11 +01:00
Brendan Tildesley
8b0e4177ee
gnu: moka-icon-theme: Simplify package definition. 
* gnu/packages/gnome.scm (moka-icon-theme): Inherit faba-icon-theme to avoid
  duplicating similar package definition.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-11-07 00:12:11 +01:00
Brendan Tildesley
d935e6a12c
gnu: Add faba-icon-theme. 
* gnu/packages/gnome.scm (faba-icon-theme): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-11-07 00:12:11 +01:00
Carlo Zancanaro
47bd32d98e
gnu: electrum: Update to 3.0. 
gnu/packages/finance.scm (electrum): Update to 3.0.
[inputs]: Change to python3 inputs.
[arguments]: Remove python-2. Disable tests.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-11-07 00:12:10 +01:00
Carlo Zancanaro
ea0421bbf6
gnu: Add python-jsonrpclib-pelix. 
* gnu/packages/python.scm (python-jsonrpclib-pelix, python2-jsonrpclib-pelix):
New variables.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
 2017-11-07 00:12:10 +01:00
Ludovic Courtès
96dc8f3527
packages: 'fold-packages' takes #:select? parameter. 
* gnu/packages.scm (fold-packages): Add #:select? parameter and honor it.
 2017-11-07 00:12:10 +01:00
Ludovic Courtès
0ad5f80982
Fix ambiguous imports. 
* gnu/packages/ocaml.scm: Hide 'zip' from (srfi srfi-1).
* guix/git.scm: Select 'mkdir-p' from (guix build utils).
 2017-11-07 00:12:10 +01:00
Efraim Flashner
913027f383
gnu: nnn: Update to 1.5. 
* gnu/packages/admin.scm (nnn): Update to 1.5.
 2017-11-06 23:07:19 +02:00
Efraim Flashner
6a534909fa
gnu: libuninameslist: Update to 20170807. 
* gnu/packages/fontutils.scm (libuninameslist): Update to 20170807.
 2017-11-06 23:07:13 +02:00
Efraim Flashner
10b159a303
gnu: u-boot: Only install 'MLO' output if it exists. 
* gnu/packages/bootloaders.scm (u-boot)[arguments]: Add 'MLO' to
uboot-files only if it has been built.
 2017-11-06 22:54:28 +02:00
Mathieu Othacehe
b1a3079347
system: vm: Use 2^32 - 1 as hash size. 
* gnu/system/vm.scm (operating-system-uuid): Use 2^32 - 1 instead of
  2^32 as hash size.

On some 32 bit system (ARM for example), 2^32 exceeds hash max
size (ULONG_MAX = 2^32 - 1).
 2017-11-06 20:02:25 +01:00
Mathieu Othacehe
dd208b936c
bootloaders: uboot: Add .img and MLO files to binary outputs. 
* gnu/packages/bootloaders.scm (make-u-boot-package): Add .img and MLO files
  as binary output.
 2017-11-06 19:58:21 +01:00
Mathieu Othacehe
f6948189a9
linux: Add omap2plus generic kernel. 
* gnu/packages/linux.scm (linux-libre-arm-omap2plus): New exported variable.
 2017-11-06 19:55:10 +01:00
Mathieu Othacehe
2ac42fe51f
gnu: uboot: Fix same-arch? check. 
* gnu/packages/bootloaders.scm (make-u-boot-package): Compare %current-system
  to system associated to given triplet. Comparing a system and a triplet
  didn't make sense.
 2017-11-06 19:53:13 +01:00
Efraim Flashner
d298e7652a
gnu: perl-test-www-mechanize-psgi: Update source uri. 
* gnu/packages/web.scm (perl-test-www-mechanize-psgi)[source]: Update to
new source uri.
 2017-11-06 20:39:45 +02:00
Efraim Flashner
12c613b548
gnu: dtc: Build python bindings. 
* gnu/packages/bootloaders.scm (dtc)[native-inputs]: Add swig.
[inputs]: Add python-2.
[arguments]: Remove 'NO_PYTHON' from make-flags, add 'SETUP_PREFIX' to
set python bindings prefix.
 2017-11-06 20:39:45 +02:00
Efraim Flashner
ab8757c5b1
gnu: dtc: Update to 1.4.5. 
* gnu/packages/bootloaders.scm (dtc): Update to 1.4.5.
[arguments]: Add NO_PYTHON flag to make-flags.
 2017-11-06 20:39:45 +02:00
Efraim Flashner
9371600ec8
gnu: libxres: Update to 1.2.0. 
* gnu/packages/xorg.scm (libxres): Update to 1.2.0.
 2017-11-06 20:02:45 +02:00
Tobias Geerinckx-Rice
fd592a12e2
gnu: youtube-dl: Update to 2017.11.06. 
* gnu/packages/video.scm (youtube-dl): Update to 2017.11.06.
 2017-11-06 18:18:41 +01:00
Efraim Flashner
8f4e3b95df
gnu: aria2: Update to 1.33.0. 
* gnu/packages/bittorrent.scm (aria2): Update to 1.33.0.
 2017-11-06 06:18:31 +02:00
Efraim Flashner
08e1f38ddd
gnu: emacs-undo-tree: Parameterize source uri. 
* gnu/packages/emacs.scm (emacs-undo-tree)[source]: Replace hard-coded
version with version parameter.
 2017-11-06 06:18:26 +02:00
Leo Famulari
73cd4022d6
gnu: borg: Update to 1.1.2. 
* gnu/packages/backup.scm (borg): Update to 1.1.2.
[arguments]: Disable another test in the 'check' phase.
 2017-11-05 20:36:05 -05:00
Eric Bavier
d8799bd0df
gnu: netsurf: Update to 3.7. 
For compatibility, dependents must be updated at the same time.

* gnu/packages/web.scm (libcss): Update to 0.7.0
(nsgenbind): Update to 0.5.
(netsurf): Update to 3.7.
[arguments]: Fix binary name in .desktop.  Adjust "docs" directory name.
* gnu/packages/patches/netsurf-system-utf8proc.patch: Adjust to new source.
 2017-11-05 07:46:08 -06:00
Eric Bavier
772588bd22
gnu: libnspsl: Update to 0.1.2. 
* gnu/packages/web.scm (libnspsl): Update to 0.1.2.
 2017-11-05 07:46:08 -06:00
Eric Bavier
f379c52f27
gnu: libnsgif: Update to 0.2.0. 
* gnu/packages/web.scm (libnsgif): Update to 0.2.0.
 2017-11-05 07:46:08 -06:00
Eric Bavier
b20d97f848
gnu: libsvgtiny: Update to 0.1.6. 
* gnu/packages/web.scm (libsvgtiny): Update to 0.1.6.
 2017-11-05 07:46:08 -06:00
Eric Bavier
036f47a37e
gnu: libdom: Update to 0.3.2. 
* gnu/packages/web.scm (libdom): Update to 0.3.2.
 2017-11-05 07:46:08 -06:00
Eric Bavier
e33f6efd60
gnu: libwapcaplet: Update to 0.4.0. 
* gnu/packages/web.scm (libwapcaplet): Update to 0.4.0.
 2017-11-05 07:46:08 -06:00
Eric Bavier
84dec7a0c0
gnu: hubbub: Update to 0.3.4. 
* gnu/packages/web.scm (hubbub): Update to 0.3.4.
 2017-11-05 07:46:07 -06:00
Eric Bavier
bf56082605
gnu: netsurf-buildsystem: Update to 1.6. 
* gnu/packages/web.scm (netsurf-buildsystem): Update to 1.6.
 2017-11-05 07:46:00 -06:00
ng0
511d8a02e8
gnu: emacs-evil: Update to 1.2.13. 
* gnu/packages/emacs.scm (emacs-evil): Update to 1.2.13.
(source): Adjust URL to new upstream location on github.
(home-page): likewise.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2017-11-05 19:23:47 +01:00
ng0
db574f7183
gnu: emacs-slime: Use correct Texinfo commands in the description. 
Previously the description had "@{something}" in it which is never
valid Texinfo. This commit changes it to use "@command{something}"
to render the full description.

* gnu/packages/emacs.scm (emacs-slime)[description]: Correct Texinfo usage.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2017-11-05 19:23:33 +01:00
ng0
77a7891b87
gnu: emacs-undo-tree: Update to 0.6.6. 
* gnu/packages/emacs (emacs-undo-tree): Update to 0.6.6.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2017-11-05 19:23:20 +01:00
ng0
5fa1b4174a
gnu: emacs-which-key: Update to 3.0.2. 
* gnu/packages/emacs.scm (emacs-which-key): Update to 3.0.2.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2017-11-05 19:22:31 +01:00
ng0
9505877205
gnu: emacs-neotree: Update to 0.5.2. 
* gnu/packages/emacs.scm (emacs-neotree): Update to 0.5.2.
[source](uri): Adjust URL to tag change.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2017-11-05 19:22:14 +01:00
Marius Bakke
aa70cf8c36
gnu: redis: Update to 4.0.2. 
* gnu/packages/databases.scm (redis): Update to 4.0.2.
 2017-11-05 19:03:32 +01:00
Rutger Helling
39f2433c39
gnu: sdl2: Update to 2.0.7 and enable Wayland backend. 
* gnu/packages/sdl.scm (sdl2): Update to 2.0.7.
[inputs]: Add wayland, wayland-protocols, libxkbcommon.
[arguments]: Add '--disable-wayland-shared' to #:configure-flags.

Co-authored-by: Marius Bakke <mbakke@fastmail.com>
 2017-11-05 18:14:19 +01:00
Gábor Boskovits
7c5cc40097
gnu: add disorderfs. 
* gnu/packages/file-systems.scm (disorderfs): New variable.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2017-11-05 17:50:48 +01:00
Gábor Boskovits
e55c46b850
gnu: python-decorator: Update to 4.1.2. 
* gnu/packages/python.scm (python-decorator): Update to 4.1.2.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2017-11-05 17:27:42 +01:00
Brendan Tildesley
743d3f6502
gnu: calibre: Install mimetypes. 
* gnu/packages/ebook.scm (calibre)[arguments]: Install mimetypes xml file.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2017-11-05 17:24:01 +01:00
Brendan Tildesley
9132212fb8
gnu: calibre: Add optipng as an input. 
* gnu/packages/ebook.scm (calibre)[inputs]: Add optipng.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2017-11-05 17:24:01 +01:00
Brendan Tildesley
bf4a40db3c
gnu: calibre: Add python2-dukpy as an input. 
* gnu/packages/ebook.scm (calibre)[inputs]: Add python2-dukpy. dukpy was
  unbundled from Calibre, so we need to to use the Guix version.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2017-11-05 17:24:01 +01:00
Brendan Tildesley
2e15906c1c
gnu: Add python-dukpy, python2-dukpy. 
gnu/packages/python.scm (python-dukpy, python2-dukpy): New variables.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2017-11-05 17:24:01 +01:00
Brendan Tildesley
7ed93a6c9e
gnu: calibre: Update to 3.11.1. 
* gnu/packages/ebook.scm (calibre): Update to 3.11.1.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2017-11-05 17:24:01 +01:00
Rutger Helling
540dd1c8cc
gnu: retroarch: Enable Wayland support. 
* gnu/packages/games.scm (retroarch)[inputs]: Add wayland.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2017-11-05 17:24:00 +01:00
Rutger Helling
ca1ddce8a3
gnu: weston: Update to 3.0.0. 
* gnu/packages/freedesktop.scm (weston): Update to 3.0.0.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2017-11-05 17:24:00 +01:00
rennes
8d2bde86ec
gnu: lollypop: Update to 0.9.304. 
* gnu/packages/gnome.scm (lollypop): Update to 0.9.304.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2017-11-05 17:24:00 +01:00
Tobias Geerinckx-Rice
08d61397cd
gnu: gnome-terminal: Update to 3.26.2. 
* gnu/packages/gnome.scm (gnome-terminal): Update to 3.26.2.
 2017-11-05 16:44:51 +01:00
Tobias Geerinckx-Rice
68488f275d
gnu: vte: Update to 0.50.2. 
* gnu/packages/gnome.scm (vte): Update to 0.50.2.
 2017-11-05 16:44:50 +01:00
Marius Bakke
7561be8699
gnu: fio: Update to 3.2. 
* gnu/packages/benchmark.scm (fio): Update to 3.2.
 2017-11-05 16:16:51 +01:00
Marius Bakke
3c41b9929b
gnu: feh: Update to 2.22. 
* gnu/packages/image-viewers.scm (feh): Update to 2.22.
[native-search-paths]: New field.
 2017-11-05 16:08:02 +01:00
Ludovic Courtès
21b71b01e9
services: Add 'description' fields. 
* gnu/services/admin.scm (rottlog-service-type)
(tailon-service-type): Add 'description' field.
* gnu/services/audio.scm (mpd-service-type): Likewise.
* gnu/services/avahi.scm (avahi-service-type): Likewise.
* gnu/services/ssh.scm (lsh-service-type)
(openssh-service-type, dropbear-service-type): Likewise.
 2017-11-05 15:29:52 +01:00
nee
b6d2930d1f
services: Add murmur. 
* gnu/services/telephony.scm: New file.
* gnu/local.mk: Add it.
* doc/guix.texi (Telephony Services): New node.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-11-05 15:21:53 +01:00
Manolis Ragkousis
50c229caf9
gnu: fio: Update to 3.1. 
* gnu/packages/benchmark.scm (fio): Update to 3.1.
 2017-11-05 12:29:46 +02:00
Hartmut Goebel
1289001a5d
gnu: prison: Move to be in alphabetical order. 
I was trapped be the definitions not being in alphabetical order.

* gnu/packages/kde-frameworks.scm (prison): Move in front of
  solid.
 2017-11-05 10:56:40 +01:00
Hartmut Goebel
a7dc855725
gnu: kdewebkit: Move to be in alphabetical order. 
I was trapped by the definitions not being in alphabetical order.

* gnu/packages/kde-frameworks.scm (kdewebkit): Move in front of
  kemoticons.
 2017-11-05 10:56:40 +01:00
Hartmut Goebel
39d1a429fe
gnu: kactivities: Move to tier 2. 
KDE now lists this package as tier 2, I was trapped by the
definitions being at the wrong place.

* gnu/packages/kde-frameworks.scm (kactivities): Move into the
  "section" of tier 2 packages. (kactivities-stats) Remove now
  obsolete comment.
 2017-11-05 10:56:39 +01:00
Hartmut Goebel
571f1fa3b2
gnu: libksysguard: Update to 5.11.2. 
* gnu/packages/kde.scm (libksysguard): Update to 5.11.2.
 2017-11-05 10:56:39 +01:00
Hartmut Goebel
e8737735a2
gnu: solid: Enable building interface for qml. 
* gnu/package/kde-frameworks.scm(solid)[inputs]: Add qtdeclarative.
 2017-11-05 10:56:38 +01:00
Hartmut Goebel
b1beb1670b
gnu: krunner: Make some tests pass. 
* gnu/packages/kde-frameworks.scm[arguments]
  <#:tests?>: Remove.
  <#:phases>[fix-paths-for-test'] New phase.
  <#:phases>[check-setup]: Set $HOME. Blacklist a failing new-in-5.39.0 test.
 2017-11-05 10:56:37 +01:00
Hartmut Goebel
5bc1efd77d
gnu: kdelibs4support: Make test kstandarddirstest pass. 
* gnu/package/kde-frameworks.scm(kdelibs4support)[#:phases]
  <check-post-install>: Add workaround for bug in test-case.
  Update comment.
 2017-11-05 10:56:36 +01:00
Hartmut Goebel
fa274ab2c0
gnu: kimageformats: Update comment. 
* gnu/packages/kde-frameworks.scm(kimageformats): Update comment.
 2017-11-05 10:56:36 +01:00
Hartmut Goebel
6211aadf4b
gnu: kde-frameworks: Update to 5.39.0. 
Beside simple updating:
- ktexteditor: Add input.
- kdelibs4support: Enable test kmimetypetest, disable test kuniqueapptest.
- kimageformats: Make the plugins available for tests.
- krunner: Make old tests pass again. Blacklist a failing new test.

* gnu/packages/kde-frameworks.scm (attica, baloo, bluez-qt, breeze-icons,
  extra-cmake-modules, kactivities, kactivities-stats, kapidox, karchive,
  kauth, kbookmarks, kcmutils, kcodecs, kcompletion, kconfig, kconfigwidgets,
  kcoreaddons, kcrash, kdbusaddons, kdeclarative, kded,
  kde-frameworkintegration, kdelibs4support, kdesignerplugin, kdesu,
  kdewebkit, kdnssd, kdoctools, kemoticons, kfilemetadata, kglobalaccel,
  kguiaddons, khtml, ki18n, kiconthemes, kidletime, kimageformats, kinit, kio,
  kitemmodels, kitemviews, kjobwidgets, kjs, kjsembed, kmediaplayer,
  knewstuff, knotifications, knotifyconfig, kpackage, kparts, kpeople,
  kplotting, kpty, kross, krunner, kservice, ksyntaxhighlighting,
  ktextwidgets, kunitconversion, kwallet, kwayland, kwidgetsaddons,
  kwindowsystem, kxmlgui, kxmlrpcclient, modemmanager-qt, networkmanager-qt,
  oxygen-icons, plasma-framework, prison, solid, sonnet, threadweaver): Update
  to 5.39.0
  (ktexteditor) Update to 5.39.0. [source]: Add patch. [inputs]: Add
  qtdeclarative.
  (kdelibs4support): Update to 5.39.0. [#:phase check-post-install]: Remove
  kmimetypetest from and add kuniqueapptest to list of test to be excluded
  when running ctest.
  (kimageformats): Update to 5.39.0. [#:phase check-setup] Make the plugins
  available for tests.
* gnu/packages/patches/ktexteditor-5.39.0-autotests-dependencies.patch:
  New file.
* gnu/local.mk (dist_patch_DATA): Register it.
 2017-11-05 10:56:35 +01:00
Hartmut Goebel
9f5bd38f94
gnu: extra-cmake-modules: Install pri-files into lib/qt5/. 
This in accordance with the documentation in
ECMGeneratePriFile.cmake: "Packagers … want to set
`ECM_MKSPECS_INSTALL_DIR` to something like
`share/qt5/mkspecs/modules`." Our Qt5 is putting pri-files into
`lib/qt5/mkspecs/modules`.

* gnu/packages/kde-frameworks.scm(extra-cmake-modules)[#:phase fix-lib-path]:
  New substitute for file 'modules/ECMGeneratePriFile.cmake'.
 2017-11-05 10:56:34 +01:00
Marius Bakke
46dea1241c
gnu: icedtea: Update to 3.6.0 [security fixes]. 
Fixes CVE-2017-{10274,10821,10825,10295,10388,10346,10350,10347,10349,10345,
10348,10357,10355,10356,10165} and CVE-2016-{10165,9840,9841,9842,9843}.

* gnu/packages/java.scm (icedtea-8): Update to 3.6.0.
[native-inputs]: Update dependency hashes.
 2017-11-04 15:33:59 +01:00
Ben Woodcroft
171ba2480f
gnu: diamond: Update to 0.9.12. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.12.
 2017-11-04 10:51:44 +10:00
Marius Bakke
d3f140218b
gnu: sssd: Disable failing test. 
* gnu/packages/sssd.scm (sssd)[arguments]<#:phases>: Add substitution to
'disable-failing-test' phase.
 2017-11-04 00:07:40 +01:00
Marius Bakke
f1ae27b608
gnu: samba: Update to 4.7.1. 
* gnu/packages/samba.scm (samba): Update to 4.7.1.
 2017-11-04 00:07:40 +01:00
Marius Bakke
ad25310dd5
gnu: ldb: Update to 1.3.0. 
* gnu/packages/samba.scm (ldb): Update to 1.3.0.
 2017-11-04 00:07:40 +01:00
Marius Bakke
d94c679254
gnu: re2: Update to 2017-11-01. 
* gnu/packages/regex.scm (re2): Update to 2017-11-01.
 2017-11-04 00:07:39 +01:00
Marius Bakke
1695bd788d
gnu: libxfont@1: Update to 1.5.3. 
* gnu/packages/xorg.scm (libxfont): Update to 1.5.3.
[source](patches): Remove.
 2017-11-04 00:07:39 +01:00
Ricardo Wurmus
66865ab8ac
gnu: multiqc: Update to 1.3. 
* gnu/packages/bioinformatics.scm (multiqc): Update to 1.3.
[propagated-inputs]: Add python-enum34.
[license]: The license was changed to "GPLv3 or later" with this release.
 2017-11-03 17:18:52 +01:00
Kei Kebreau
416ad6feaa
gnu: iso-codes: Update to 3.76. 
* gnu/packages/iso-codes.scm (iso-codes): Update to 3.76.
 2017-11-03 09:34:13 -04:00
Ricardo Wurmus
b12c6a664d
gnu: r-ape: Update to 5.0. 
* gnu/packages/bioinformatics.scm (r-ape): Update to 5.0.
[propagated-inputs]: Add r-rcpp.
 2017-11-03 14:14:38 +01:00
Ricardo Wurmus
840782204f
gnu: r-bbmle: Update to 1.0.20. 
* gnu/packages/cran.scm (r-bbmle): Update to 1.0.20.
 2017-11-03 14:14:38 +01:00
Ricardo Wurmus
1a1b4f0571
gnu: r-proxy: Update to 0.4-19. 
* gnu/packages/cran.scm (r-proxy): Update to 0.4-19.
 2017-11-03 14:14:38 +01:00
Ricardo Wurmus
a8a2871f71
gnu: r-glue: Update to 1.2.0. 
* gnu/packages/cran.scm (r-glue): Update to 1.2.0.
 2017-11-03 14:14:38 +01:00
Ricardo Wurmus
a6ec5b7043
gnu: r-withr: Update to 2.1.0. 
* gnu/packages/statistics.scm (r-withr): Update to 2.1.0.
[propagated-inputs]: Add r-lattice.
 2017-11-03 14:14:37 +01:00
Ricardo Wurmus
fd9afcf4ea
gnu: r-quantreg: Update to 5.34. 
* gnu/packages/statistics.scm (r-quantreg): Update to 5.34.
 2017-11-03 14:14:37 +01:00
Ricardo Wurmus
1fe75660c0
gnu: r-robustbase: Update to 0.92-8. 
* gnu/packages/statistics.scm (r-robustbase): Update to 0.92-8.
 2017-11-03 14:14:37 +01:00
Ricardo Wurmus
1fb415cb50
gnu: r-purrr: Update to 0.2.4. 
* gnu/packages/statistics.scm (r-purrr): Update to 0.2.4.
 2017-11-03 14:14:37 +01:00
Ricardo Wurmus
c8818f5577
gnu: r-irlba: Update to 2.3.1. 
* gnu/packages/statistics.scm (r-irlba): Update to 2.3.1.
 2017-11-03 14:14:37 +01:00
Ricardo Wurmus
116e9837b5
gnu: r-checkmate: Update to 1.8.5. 
* gnu/packages/statistics.scm (r-checkmate): Update to 1.8.5.
 2017-11-03 14:14:36 +01:00
Ricardo Wurmus
fde66e3018
gnu: r-multitaper: Update to 1.0-14. 
* gnu/packages/statistics.scm (r-multitaper): Update to 1.0-14.
 2017-11-03 14:14:36 +01:00
Ricardo Wurmus
0a123e0609
gnu: r-data-table: Update to 1.10.4-3. 
* gnu/packages/statistics.scm (r-data-table): Update to 1.10.4-3.
 2017-11-03 14:14:36 +01:00
Ricardo Wurmus
b5a2f37157
gnu: r-pryr: Update to 0.1.3 
* gnu/packages/statistics.scm (r-pryr): Update to 0.1.3.
 2017-11-03 14:14:36 +01:00
Ricardo Wurmus
bc409c8d3b
gnu: r-lazyeval: Update to 0.2.1. 
* gnu/packages/statistics.scm (r-lazyeval): Update to 0.2.1.
 2017-11-03 14:14:36 +01:00
Ricardo Wurmus
6b968c4cd3
gnu: Add r-corrplot. 
* gnu/packages/cran.scm (r-corrplot): New variable.
 2017-11-03 10:34:24 +01:00
Ricardo Wurmus
81e0b62502
gnu: Add r-ggrepel. 
* gnu/packages/cran.scm (r-ggrepel): New variable.
 2017-11-03 10:34:23 +01:00
Mark H Weaver
0f3142e7c3
gnu: linux-libre: Update to 4.13.11. 
* gnu/packages/linux.scm (%linux-libre-version): Update to 4.13.11.
(%linux-libre-hash): Update hash.
 2017-11-03 01:31:06 -04:00
Mark H Weaver
336b8d422d
gnu: linux-libre@4.9: Update to 4.9.60. 
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.60.
 2017-11-03 01:30:25 -04:00
Mark H Weaver
15d44dfe22
gnu: linux-libre@4.4: Update to 4.4.96. 
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.96.
 2017-11-03 01:29:33 -04:00
Oleg Pykhalov
72df48dbad
gnu: Add kodi-cli. 
* gnu/packages/kodi.scm (kodi-cli): New variable.
 2017-11-03 06:46:03 +03:00
Ricardo Wurmus
1d84500a72
gnu: conda: Fix environment scripts. 
* gnu/packages/package-management.scm (conda)[arguments]: Add phase
"undo-wrap".
 2017-11-03 00:12:46 +01:00
Marius Bakke
ada53b1d50
Revert "gnu: itstool: Update to 2.0.4." 
This reverts commit 13fbd174b5.
 2017-11-02 23:00:23 +01:00
Marius Bakke
77576be41f
gnu: openssl@1.1: Update to 1.1.0g [fixes CVE-2017-3735, CVE-2017-2736]. 
* gnu/packages/tls.scm (openssl-next): Update to 1.1.0g.
[source]: Add HTTPS mirror.
 2017-11-02 22:21:59 +01:00
Marius Bakke
1df4f5c919
gnu: openssl@1.0: Replace with 1.0.2m [fixes CVE-2017-3735, CVE-2017-2736]. 
* gnu/packages/tls.scm (openssl)[replacement]: New field.
(openssl-1.0.2m): New public variable.
 2017-11-02 22:21:59 +01:00
Efraim Flashner
22bf67d1f4
gnu: enlightenment: Update to 0.22.0. 
* gnu/packages/enlightenment.scm (enlightenment): Update to 0.22.0.
 2017-11-02 23:05:11 +02:00
Efraim Flashner
41b5408235
gnu: efl: Update to 1.20.5. 
* gnu/packages/enlightenment.scm (efl): Update to 1.20.5.
 2017-11-02 23:05:09 +02:00
Marius Bakke
bc183968f5
gnu: vte-ng: Update to 0.50.2.a. 
* gnu/packages/gnome.scm (vte-ng): Update to 0.50.2.a.
 2017-11-02 21:17:41 +01:00
Tobias Geerinckx-Rice
52995941bc
gnu: gnome-todo: Update to 3.26.2. 
* gnu/packages/gnome.scm (gnome-todo): Update to 3.26.2.
 2017-11-02 21:10:21 +01:00
Tobias Geerinckx-Rice
92c9392767
gnu: dconf-editor: Update to 3.26.2. 
* gnu/packages/gnome.scm (dconf-editor): Update to 3.26.2.
 2017-11-02 21:10:21 +01:00
Tobias Geerinckx-Rice
b39e612115
gnu: gnome-clocks: Update to 3.26.1. 
* gnu/packages/gnome.scm (gnome-clocks): Update to 3.26.1.
 2017-11-02 21:10:20 +01:00
Tobias Geerinckx-Rice
1b59d45ee4
gnu: file-roller: Update to 3.26.2. 
gnu/packages/gnome.scm (file-roller): Update to 3.26.2.
 2017-11-02 21:10:20 +01:00
Tobias Geerinckx-Rice
46994d0d4c
gnu: aisleriot: Update to 3.22.4. 
* gnu/packages/gnome.scm (aisleriot): Update to 3.22.4.
 2017-11-02 21:10:19 +01:00
Tobias Geerinckx-Rice
03e775d4e8
gnu: knot: Update to 2.6.1. 
* gnu/packages/dns.scm (knot): Update to 2.6.1.
 2017-11-02 21:10:18 +01:00
Tobias Geerinckx-Rice
73b80ff924
gnu: miniupnpc: Update to 2.0.20171102. 
* gnu/packages/upnp.scm (miniupnpc): Update to 2.0.20171102.
 2017-11-02 21:10:18 +01:00
Rutger Helling
3440f12a7e
gnu: mpv: enable Wayland support. 
* gnu/packages/video.scm (mpv)[inputs]: Add wayland and libxkbcommon.
 2017-11-02 16:03:25 -04:00
Kei Kebreau
13fbd174b5
gnu: itstool: Update to 2.0.4. 
* gnu/packages/glib.scm (itstool): Update to 2.0.4.
[inputs]: Replace python and python-libxml2 with python-2 and python2-libxml2.
 2017-11-02 15:37:22 -04:00
Kei Kebreau
67bd376b1a
gnu: gnome-maps: Update to 3.26.2. 
* gnu/packages/geo.scm (gnome-maps): Update to 3.26.2.
[arguments]: In 'install' phase, add webkitgtk to LD_LIBRARY_PATH.
 2017-11-02 14:42:58 -04:00
Kei Kebreau
4dd137d508
gnu: libgweather: Update to 3.26.0. 
* gnu/packages/gnome.scm (libgweather): Update to 3.26.0.
 2017-11-02 12:05:03 -04:00
Julien Lepiller
bb27eb0dbf
gnu: Add java-plexus-classworlds. 
* gnu/packages/java.scm (java-plexus-classworlds): New variable.
 2017-11-02 13:07:38 +01:00
Julien Lepiller
4d50897515
gnu: Add java-powermock-api-easymock. 
* gnu/packages/java.scm (java-powermock-api-easymock): New variable.
 2017-11-02 13:07:30 +01:00
Julien Lepiller
33db168181
gnu: Add java-powermock-modules-junit4. 
* gnu/packages/java.scm (java-powermock-modules-junit4): New variable.
 2017-11-02 13:07:27 +01:00
Julien Lepiller
6c21d46c70
gnu: Add java-powermock-modules-junit4-common. 
* gnu/packages/java.scm (java-powermock-modules-junit4-common): New
variable.
 2017-11-02 13:07:24 +01:00
Julien Lepiller
2d5d65d7dd
gnu: Add java-powermock-api-support. 
* gnu/packages/java.scm (java-powermock-api-support): New variable.
 2017-11-02 13:07:22 +01:00
Julien Lepiller
d4a4d5da60
gnu: Add java-powermock-core. 
* gnu/packages/java.scm (java-powermock-core): New variable.
 2017-11-02 13:07:19 +01:00
Julien Lepiller
8d6a48150a
gnu: Add java-powermock-reflect. 
* gnu/packages/java.scm (java-powermock-reflect): New variable.
* gnu/packages/patches/java-powermock-fix-java-files.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
 2017-11-02 13:07:17 +01:00
Julien Lepiller
5619556b24
gnu: Add java-xerial-core. 
* gnu/packages/java.scm (java-xerial-core): New variable.
 2017-11-02 13:07:15 +01:00
Julien Lepiller
a53d9ac0f2
gnu: Add java-lmax-disruptor. 
* gnu/packages/java.scm (java-lmax-disruptor): New variable.
 2017-11-02 13:07:12 +01:00
Julien Lepiller
3120836732
gnu: Add java-bouncycastle-bcpkix. 
* gnu/packages/java.scm (java-bouncycastle-bcpkix): New variable.
 2017-11-02 13:07:09 +01:00
Julien Lepiller
62315865df
gnu: Add java-bouncycastle-bcprov. 
* gnu/packages/java.scm (java-bouncycastle-bcprov): New variable.
 2017-11-02 13:07:07 +01:00
Julien Lepiller
d54d7d31ac
gnu: Add java-lz4. 
* gnu/packages/java.scm (java-lz4): New variable.
 2017-11-02 13:07:04 +01:00